I do not permanently delete books. I do have an archive library, but that's to store originals of omnibuses / collections that I split into individual books, that sort of thing. My main library has search filters that I use to hide / show books I've already read, books I marked as did-not-finish, etc...

This is the same thing that I do with EpubSplit. It's good to know someone else is doing what I am doing with the books that I have split.